Getting fastq files as the output of bowtie2
2
0
Entering edit mode
6 weeks ago
Sara ▴ 200

I am trying to use bowtie2 to filter out rRNs from my RNAseq data and as output I would like to get 2 fastq files:

  1. clean data (my RNAseq data without rRNAs reads)
  2. rRNAs reads that are removed from my RNAseq fastq file

All the commands that I found return sam or bam files. How can I get such fastq files using bowtie2?

bowtie2 • 232 views
ADD COMMENT
0
Entering edit mode

Reach out to your core and ask them if they did ribodepletion step.

ADD REPLY
0
Entering edit mode
6 weeks ago

bam2fastq/sam2fastq may help you.

ADD COMMENT
0
Entering edit mode
6 weeks ago

I am going to address what you are after rather than what you are asking (known as the XY Problem), read this post:

Cleaning RNA-Seq data from rRNA

the TLDR is:

You could use a tool like SortMeRna https://bioinfo.lifl.fr/RNA/sortmerna/

Or not do anything at all and carry on with the analysis,

ADD COMMENT

Login before adding your answer.

Traffic: 2047 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6